On The Run
by Multifangirlll
Summary: Young Sam and Dean have experienced a lot. But they never heard of something like the flare. Until they were taken by W.I.C.K.E.D. Will they make new friends, enemies, or more importantly, a way out. Rated T for Dean language. Hope you enjoy :)
1. Chapter 1

_A/N: hi guys, well, first of all, this is my first FanFiction so please go easy on me. Also, I'm not English so there could be some language mistakes. I'll be updating chapters if I can figure out how. Hopefully you'll enjoy :)_

 **I don't own Supernatural or The Maze Runner.**

It had been years since the fire. John was still searching for the thing that had killed Mary and Sam and Dean were left alone in another motel room. Sam was about 12 and Dean just turned 16. But lately something strange had happened. Random people were infected with some kind of monster infection. People called it the flare. Somehow Sam and Dean were immune. They had been hunting some cases but until John could figure out what that thing was, the brothers were demanded to stay inside that motel room. John had seen things. Children being stolen by people, or what he thought were people. And after Mary, he couldn't bear to lose his sons too. Only Dean, could sometimes go outside just to get some food and basic stuff.

It had gotten pretty lonely for the boys. Sam wanted to go to school again and Dean wanted to go hunting. Their father hadn't come back in days now and they started to worry, especially because the flare would usually just take adults.

"When is he coming back, Dean?" Sam asked worried.

"Patience Sammy, he'll make it." Dean said trying to calm his brother, even though he was pretty scared himself. But he wasn't going to show that.

When another silence was about to cross to room, they heard a knock on the motel room door. Sam and Dean looked at each other in surprise.

 _Could that be him? He wouldn't knock would he?_

Slowly, Dean walked to the door and tried to look through the peephole. He saw two men standing outside in white quarantine suits. It couldn't be some kind of monster so Dean opened the door in a small peek. The men were staring at him.

"Can I help you?" Dean asked.

"Are you in there alone?" One of them asked.

 _What was that question supposed to mean? Who were these people?_

By Dean's hesitation the men noticed he wasn't alone and kept asking.

"Is it okay if we come in to explain ourselves?" The other one asked.

"Well, not really, I was helping my brother with some homework. Maybe later. Bye bye."

Dean was about to close to door when the man put his foot between it. Dean saw a W.I.C.K.E.D logo on the suits of the strangers.

"Actually, it's really urgent." The man said.

"I said-" at that moment the men broke in. Before Dean could grab a gun or something he was already surrounded by the stranger. The other man walked in and said: "you were right, there are two of them in here." In some kind of microphone. More man came in a few seconds later and Dean looked over to Sam. The strangers were coming at him and he was standing in a corner. Not at all insecure or anything, but constantly looking at Dean. Dean himself managed to knock the first man out, but there were too many. When one of them was holding his arms from behind, he saw Sam was being captured too.

"Look kids, we just want to talk." Said one of them.

"Yeah well, then talk!" Dean responded in and sarcastically angry tone.

"Who are you?" Sam asked.

"Our organization is called W.I.C.K.E.D and we only want to help."

"Where are your parents?" Another W.I.C.K.E.D guy asked.

"You keep talking, we don't have to tell you anything." Dean said.

"They'll be back very soon." Sam added.

"Then we have to be quick." The stranger said and he turned to Sam and Dean again.

"I didn't want it to go this way, but if you boys don't want to come with us, we have to make you."

Sam looked at Dean, scared. Dean was still processing what was going on and before he knew there was a black bag over his head and he couldn't see anything.


	2. Chapter 2

_A/N: Hi! I apologize, this is an incredibly short chapter, the next one will hopefully be some longer. I'll get to the actual crossover part next chapter. Enjoy!_

The brothers were sitting in a moving car, still unable to see anything with a bag over their heads. Sam had tried to count how look the ride took, like he learned from his dad. But it was a very long ride and unfortunately he had lost count. He tried not to be scared, Dean would only make fun of him. But he was petrified.

The car stopped and Sam felt someone pulling him out. He called out.

"Dean?"

"It's going to be okay Sammy, I'll get us out of here." Dean voice went softer, further away. They were being separated.

…

When Dean's bag was being removed from his head, he was laying on a cold table. People were standing around him. He couldn't see what was going on, he was being tied down, he had one free hand though. He felt that they were searching him for knives or something. He heard people around him talking.

"He's a sixteen year old kid! He wouldn't have any weapons on him!"

"It's Dean Winchester." Then everyone was silent.

He saw some woman pulling his watch off, then she grabbed the chord of his necklace, wanting to take that off too. Dean putt his hand on the necklace pressing it to his chest.

"No." He said in an angry tone.

"I'm sorry kid, we have to."

"Oh come on! It's way too small for a hidden gun or knife or something in there right?"

He was silent for a few seconds.

"Please, I need to keep this." He was still holding the Samulet to his chest.

The woman walked away. Dean started looking around, searching for his brother. Sam was nowhere to be found. He tried to ask some of these doctors, but no one was kind enough to give him some answers. They were all just ignoring him. Suddenly he felt a terrible pain in his head. People were doing something to his brain. A few seconds later everything went black.


	3. Chapter 3

**A/N: Hello to anyone who's reading this, so this chapter is longer than the last one, but I should probably say something: this story is not exactly how The Maze runner or Supernatural is supposed to go, there are changes. I try to keep some details in, but the big plots and Thomas's rol is different. Anyway, hope you enjoy and please comment if you like it or something.**

 _"You told him?!" John was angry, he just came back from a hunt to hear Dean's news. Dean knew this moment like it was yesterday. When it was actually a couple of years ago, a few days after Christmas. "Dad, he kept asking questions about why we move around so much!" Dean replied. He felt guilty. His one job: looking out for Sammy. And now Sam knew everything, about the hunting, the monsters, the family business. He broke his promise to his dad and more importantly, Sammy wasn't safe anymore. It was Dean's own choice to tell their dad about it, he had to be honest, but he could've made it a lot easier to himself if he would just tell John that Sam had found the journal and Dean had to tell him what it was. That was in fact what really happened, but John would get angry at Sam, who was sleeping peacefully in the other room, for looking through his stuff. "I can't believe this, Dean." John continued. Dean looked at the ground. "I'm really sorry, dad. I'm really, really sorry." He kept saying. A tear was running down his face._

 _John screamed at Dean for another ten minutes. Dean just listened through it and nodded quietly. Then they heard the door crackle and they were both quiet. After a few seconds Sammy was standing in the doorway. "What's all that noise, Dean?" He asked while rubbing his eyes. Then he realized his dad was home. "Dad!" Sam jumped in John's arms and John laughed. "Hey buddy! How are you?" "Great! Dean and I did Christmas presents, I got girl presents but we went to exchange it." Sam replied filled with excitement. "That's great, I'd like to hear all about it, but it's way past your bedtime and I'm pretty tired too so why don't we all go to sleep first." John put Sam back on the ground. "But I don't think I can sleep anymore." Sam replied. "Dean will go to sleep too." John said, while looking at Dean. Dean nodded, he was glad that he could go away from the screaming and go to his bed._

 _Dean tugged Sam in, Sam knew he was old enough to tell Dean that he didn't need that anymore and that he could do it himself, but he was silent. When Dean was in his bed too, Sam started talking. "So you told dad that you told me right?"_

 _"You heard that?"_

 _"Yeah, you guys were pretty loud..." Both brothers were silent for a few seconds before Sam began to speak again._

 _"Dean?"_

 _"Yeah?"_

 _"What did mom do when we couldn't sleep?" Sam asked, laying on his back, staring at the ceiling._

 _"She'd tell us to shut up." Dean joked. When Sam was silent, Dean continued._

 _"She would sing 'Hey Jude' to us."_

 _"Really?"_

 _"It was her favorite Beatles song." Dean felt strange talking about their mother, but he felt that he had to tell those things to Sam. To keep her memories alive._

 _"And she'd tell us that everything was going to be alright."_

 _"Is it?" Sam asked, half asleep and calmed by the thought._

 _"Yes." Dean looked over to Sam, who was now fully unconscious._

 _He smiled._

 ** _"_** **Everything is going to be alright.** ** _"_**

Dean's eyes flew open. He was in a sort of moving box, like an elevator, but less fancy. He felt horrible, dizzy, like he was going to throw up. Then the box stopped moving. Some sort of doors opened and he saw a bright light. Once he could actually see through it, he saw people standing around him. Quietly, he stared at the faces in a questioning look. Some black haired boy jumped inside the box and raised his hand.

"First day Greenie, rise and shine." The boy said. Dean didn't know what to think. A blond boy spoke in a British accent from behind the crowd.

"Do you remember anything? Your name? Your Family?"

"I'm Dean, but-"

"Sam.." Dean whispered. "Where's Sam?"

The boys looked at him with him with surprised faces, like they didn't expect him to know anything. Dean ignored it. He looked around. With the light, he saw that he was laying in a box full of stuff, like supplies. He didn't know what the heck this all meant. He was still searching for Sam when the black haired boy, who had jumped into the box before, began to talk again.

"You remember your name?"

"Of course I do, what is..." Dean was searching for his words in panic.

"What the hell is going on? What is this? Who are you guys? Where is Sam!" He continued.

"Well let's start again than shall we, I'm Thomas, the previous Greenie." The black haired boy said.

"Greenie?" Dean asked with a sarcastic tone.

"You'll learn our language soon enough, for now, you can get some rest." Thomas replied. Dean nodded. He did feel pretty tired, and it wasn't like Sam could've hidden himself inside that box with Dean, so he followed some boys to a place they called 'Homestead'. When he looked back, he saw Thomas talking to the British, blond boy.

"I did good right, for the first time greeting a new Greenie?" Dean heard Thomas say.

"Yeah sure," the other boy replied. "But don't you think there's something strange about him? He remembers his name, and some Sam?"

"We should keep an eye on him in case-" Dean couldn't hear the rest. But he knew that they sure weren't the only ones who were going to keep an eye on things.

Dean was picking his hammock in the Homestead, he was observing, he really didn't trust anyone. He looked around him and saw a younger boy, around Sam's age and another older boy screaming at him. He was just about to go and stand up for the younger boy when the British boy broke it already. He must be some kind of leader of this group, Dean thought. After a few seconds, the blond boy came up to him.

"I'm Newt." He said. "Sorry for what you had to see back there, Gally's always angry at people, especially at Chuck. But I promise, it is pretty peaceful out here." he held out his hand.

"Dean." He shaked Newt's hand.

"So how has it been in the glade so far, eh?" Newt continued.

"Fantastic." Dean said sarcastically. He didn't really know what 'glade' meant. But he thought it would probably mean where they all live.

"About that," Dean stopped moving and turned his head to Newt, who looked surprised at Dean's grumpiness. "I want to know what the hell is going on here so tell me. Everything." Dean said, getting straight to the point. Newt hesitated for a moment but eventually, he started talking. "Like I said, this place is called the glade. Every week, the box comes up, delivering supplies to us and once a month, a new Greenie."

"And what are those?" Dean pointed at the stone walls that seemed to surround the whole glade. "It's more like, what's behind it?" Newt said before continuing. "The glade is built inside a big Maze. Now, everyday when those doors open, our runners go out there, trying to find an exit to get us all out of this place. They have to be back before sundown because that's when the walls close again and no one's ever survived a night in the maze." Both boys were silent. Dean looked at the terror at Newt's face and decided that that was enough information for today. He wanted to go and lay in his hammock but Newt stopped him. "Wait a sec, mate! There is a party planned for ya!"

Dean was sitting against a log of wood. He looked at the sky, sundown. Newt was right. A few boys ran through the enormous doors, looking like they had ran all day. Others were preparing a bonfire for him. A chubby, brown haired, young boy came up to him and sat beside him. "Chuck, was it?" Dean asked.

"Yeah! And you're Dean, right?" He replied. Dean nodded.

"Newt said he explained some things to you."

"Yes. He did." Dean said.

"Can I ask you something?" Chuck turned his head.

"You're already asking something." Dean replied. Chuck surely didn't understand Dean's sarcasm because he was silent. "Go ahead." Dean said after a few seconds.

"Do you remember your parents?" Chuck asked.

Now Dean was the one who was quiet. He didn't really wanna talk about it, but he did remember. He remembered everything. He was just about to open his mouth when a familiar sound was heard. The box. He looked at Chuck, who looked just as surprised as himself.

Dean and Chuck were running towards the box and Dean made his way through the crowd. Newt was already opening the doors. Dean was curious, but also really confused. He thought the box only came up once a week, not twice a day? Dean was the first one to be able to look what was inside the box, and by seeing that, he gasped.

"Sam!"

The twelve year old laid there, unconscious. Newt was about to jump into the box, but Dean was already inside. He grabbed his brother's pulse and searched for a heartbeat. He was relieved when he found it. "He's alive." He said, turning his head to the other boys. They were looking at him like he was the weirdest person they had ever met.

"You know him?" Thomas asked.

"Yeah I 'know' him, he's my brother!" Dean said, now the boys were looking at him even stranger. He didn't care and turned his head to Sam again.

"It's okay Sammy, I got you." He said.

 **"Everything is going to be alright."**


	4. Chapter 4

_A/N: Hi guys! Chapter 4 already, never would've expected that I would write a FanFiction in the first place, but I'm glad I did. So here's the next chapter, please review. Hope you enjoy._ _PS: I'm really sorry, I reread my earlier chapters and there are some big mistakes in which I didn't notice when I wrote/checked it._

Dean was sitting in a little cabin, thinking about what had been going on. Sam lay next to him, still unconscious. He was waiting for hours now. Dean was worried, when he came up the box, he was awake, why wouldn't Sam be? He heard someone entering the little cabin people called the medjacks. When he looked to see who it was, he didn't recognize the boy.

"Geez, how many of you are there?" Dean said with annoyance in his voice.

"Well that's a good way to start a conversation, nice meeting you too." The boy said.

Dean looked at the boy with a questioning expression, he certainly didn't expect that answer.

"Yes, greenie?" Dean didn't answer.

"I'm Minho by the way, in case you were wondering."

"Dean." He said in a grumpy tone, turning his head to Sam again. Minho sat on the chair next to him. He began trying to start a conversation.

"Two greenies in one day, that's strange you know?" Minho stated. Silence.

"Chuck said you remembered stuff." Silence again.

"So that's your brother?" Minho asked still trying to start a conversation.

"Look, I really don't need your sympathy, okay? I just want to go home again." Dean said louder.

"Okay okay, you made that clear but I was only trying to help. You know, at least you have a home and a brother! We don't remember anything!" Minho said angrily. He stood up to leave, but stopped in the doorway.

"Go get some sleep, maybe you wouldn't be so cranky. I'm sure your brother will be here when you wake up in the morning." And he left.

Dean felt kind of guilty, but he really didn't want to talk to anyone. He looked at Sam once again, but saw something new this time. There was a small piece of paper in Sam's hoodie pocket. Dean grabbed it and folded it open.

' _You better start worrying about this._ ' It said. Hadn't he had enough confusion today? Now this. He decided to keep this a secret for a while just in case anyone would think it was his or Sam's fault, it couldn't be that big a deal. He was thinking about Minho's advice. Some sleep didn't sound so bad. Just as he was about to lay down on a bed he heard a soft voice from behind.

"Dean?"

Dean looked around to see Sam half awake trying to stand up while rubbing his eyes.

"Sammy! Thank god, you're awake." Dean jumped up to hug his brother.

"What's going on? Where are we?" Sam hugged Dean back, but looked around.

"I'll explain later, how much do you remember?" Dean asked, letting go of Sam.

"Well," Sam explained. "I was in a moving car or something with you, then I was pulled out and when the bag was removed from my head, I was sitting on a cold table. People were staring really creepy at me and I asked them where you were. They said..." Sam stopped in hesitation.

"What? Come on Sammy, what happened?"

"Well they said not to tell any of you..."

Dean was getting a little angry. "What? Why would they tell you that?" He stopped talking for a second. "You trust me, right?!"

"Yes, of course.."

"So?"

"Calm down, well.. They said that we were send here for a reason.."

"And that is...?"

"I don't know, okay. They just told that to me, and that I couldn't tell anyone. Oh, and one other thing before everything went black, a woman told me that Wicked is good." Dean was silent for a moment while Sam sat down on the bed. "What is this place, Dean?

"Well, I'll tell you tomorrow, you have to get some sleep first." Dean said.

"But I just woke up?"

"Yeah well... You have to get double sleep for.. Health! Yes, health."

"Dean, you know that doesn't make sense."

"Yeah? Well, how would you know? Besides, I'm the oldest and means I'm right."

Sam sighed. He was a little tired, defiantly too tired to argue with Dean. He laid down on the bed and his closed eyes.

"See? Goodnight, Sammy." Dean said smiling and he went to sleep himself.

Sam woke up by a bright light of the morning. He looked over to Dean, who was still sleeping. He decided not to wake him up thinking about how tired Dean looked the other day. Sam felt strange, he had no idea where he was nor what was going on. He walked outside just to see a big field with boys walking around in it. It kind of looked like a survival reality show. He kept looking around, the boys walking were all doing their own thing, there were some working in a garden, some preparing food and others were doing something with animals walking around. Other than people there was a forest, or at least a lot of trees, and on the other side an enormous wall. Sam slowly walked towards it trying to figure out what it was. _Why would there be a wall in the middle of a field?_ He thought while walking. When closer to the wall, he saw that there wasn't only one wall, there were four, all surrounding the field. There seemed to be one escape through the walls. Since no one seemed to notice him, Sam walked towards the only opening.

"Hey! You!" Someone yelled at him and Sam saw a person running towards him.

He didn't trust anyone at the moment, except for Dean, anyone could be a demon. He ran away from the boys, right through the opening.


End file.
